I didn't add anything like this. This program, as its description suggests, generates configs for a full mesh network. I.e., every node has a direct connection with every other node. Once you start to want to make exceptions or edit a particular connection, the editor becomes magnitudes more complex.

The easier approach at that point would be to build some kind of a UI and you can drag a line between nodes to create a connection or remove a line to break that direct connection, but that's going to take a lot longer to write.

I understand that wg-meshconf should not support all possible configurations, but I think my specific use case is very common, and easy to achieve without any modifications to the database or API.

The proposed logic is:

a = (the node for which we are currently generating a config file)
b = (peer for which we are currently generating a [Peer] section in the config file)

a_can_see_b_directly = (a has an endpoint) && (b has an endpoint)

if !a_can_see_b_directly
    do not write AllowedIPs
end if

I wrote this on the PR, but I think that this sort of config is still useful. Without manual editing, NAT -> NAT routing will not be optimized, but it will work so long as you set allowedIPs on one connectable client to include the wg IPs of all NAT devices.

For many people, this is likely fine.